This gene is a member of the plant homeodomain (PHD)-like finger (PHF) family. It encodes a protein with two PHD-type zinc finger domains, indicating a potential role in transcriptional regulation, that localizes to the nucleolus. Mutations affecting the coding region of this gene or the splicing of the transcript have been associated with Borjeson-Forssman-Lehmann syndrome (BF... See more...

Aliases for PHF6 Gene

Aliases for PHF6 Gene

  • PHD Finger Protein 6 2 3 4 5
  • PHD-Like Zinc Finger Protein 3 4
  • Centromere Protein 31 2 3
  • CENP-31 3 4
  • Borjeson-Forssman-Lehmann Syndrome 2
  • KIAA1823 4
  • BFLS 3
  • BORJ 3

External Ids for PHF6 Gene

Previous HGNC Symbols for PHF6 Gene

  • BFLS
  • BORJ

Previous GeneCards Identifiers for PHF6 Gene

  • GC00U991174
  • GC0XP130353
  • GC0XP131452
  • GC0XP132212
  • GC0XP133232
  • GC0XP133334
  • GC0XP133507
  • GC0XP122905

Summaries for PHF6 Gene

Entrez Gene Summary for PHF6 Gene

  • This gene is a member of the plant homeodomain (PHD)-like finger (PHF) family. It encodes a protein with two PHD-type zinc finger domains, indicating a potential role in transcriptional regulation, that localizes to the nucleolus. Mutations affecting the coding region of this gene or the splicing of the transcript have been associated with Borjeson-Forssman-Lehmann syndrome (BFLS), a disorder characterized by cognitive disability, epilepsy, hypogonadism, hypometabolism, obesity, swelling of subcutaneous tissue of the face, narrow palpebral fissures, and large ears. Alternate splicing results in multiple transcript variants, encoding different isoforms. [provided by RefSeq, Jun 2010]

GeneCards Summary for PHF6 Gene

PHF6 (PHD Finger Protein 6) is a Protein Coding gene. Diseases associated with PHF6 include Borjeson-Forssman-Lehmann Syndrome and Gynecomastia. Among its related pathways are Mesodermal Commitment Pathway. Gene Ontology (GO) annotations related to this gene include histone binding. An important paralog of this gene is PHF11.

UniProtKB/Swiss-Prot Summary for PHF6 Gene

  • Transcriptional regulator that associates with ribosomal RNA promoters and suppresses ribosomal RNA (rRNA) transcription.

Gene Wiki entry for PHF6 Gene

Additional gene information for PHF6 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PHF6 Gene

Genomics for PHF6 Gene

GeneHancer (GH) Regulatory Elements for PHF6 Gene

Promoters and enhancers for PHF6 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XJ134372 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 509.4 +1.2 1232 4.2 ZBTB40 ZNF217 NRF1 POLR2G PHF8 ZFX POLR2A ZBTB10 ZBTB26 TOE1 PHF6 lnc-HPRT1-7 RF00017-8730
GH0XJ134459 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 10.7 +87.3 87348 2.4 NRF1 PHF8 POLR2A ZBTB26 REST MYC CHD1 CTBP1 ZNF341 SIN3A HPRT1 FAM122B PHF6 RF00017-8732 RF00017-8731 RF00017-8730
GH0XJ133444 Promoter/Enhancer 1.2 ENCODE CraniofacialAtlas dbSUPER 11.6 -927.8 -927808 1.1 ZNF217 TRIM28 ZBTB17 ZKSCAN1 ZNF76 ZNF184 ZNF335 ZNF512B ZNF189 HIC1 GPC4 PHF6 RF00017-8722 piR-38580-424
GH0XJ134570 Enhancer 0.9 Ensembl ENCODE 5.1 +198.7 198738 4.4 TCF12 ZIC2 TRIM28 NFIC ZNF263 FOSL2 ZNF592 PBX2 NR3C1 JUND MIR503HG LINC00629 MIR503 MIR450A1 MIR450A2 MIR450B MIR542 PHF6 RF00017-8731 ENSG00000235813
GH0XJ134171 Promoter/Enhancer 2 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 1.9 -200.1 -200134 5.8 MYC USF1 ZIC2 ZBTB10 ZBTB26 HDAC2 POLR2A SP2 MXI1 ZNF76 ENSG00000283638 CCDC160 GPC3 PHF6 MIR106A
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PHF6 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PHF6

Top Transcription factor binding sites by QIAGEN in the PHF6 gene promoter:
  • AML1a
  • FOXD3
  • HNF-4alpha1
  • HNF-4alpha2
  • NF-kappaB
  • NF-kappaB1
  • POU3F2
  • Sox9
  • Sp1

Genomic Locations for PHF6 Gene

Genomic Locations for PHF6 Gene
chrX:134,373,253-134,428,792
(GRCh38/hg38)
Size:
55,540 bases
Orientation:
Plus strand
chrX:133,507,283-133,562,822
(GRCh37/hg19)
Size:
55,540 bases
Orientation:
Plus strand

Genomic View for PHF6 Gene

Genes around PHF6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PHF6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PHF6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PHF6 Gene

Proteins for PHF6 Gene

  • Protein details for PHF6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8IWS0-PHF6_HUMAN
    Recommended name:
    PHD finger protein 6
    Protein Accession:
    Q8IWS0
    Secondary Accessions:
    • A8K230
    • B4E0G4
    • D3DTG3
    • E9PC97
    • Q5JRC7
    • Q5JRC8
    • Q96JK3
    • Q9BRU0

    Protein attributes for PHF6 Gene

    Size:
    365 amino acids
    Molecular mass:
    41290 Da
    Quaternary structure:
    • Interacts with UBTF. Interacts with the NuRD complex component RBBP4 (via the nucleolar localization motif), the interaction mediates transcriptional repression activity.
    SequenceCaution:
    • Sequence=BAB47452.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PHF6 Gene

    Alternative splice isoforms for PHF6 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PHF6 Gene

Post-translational modifications for PHF6 Gene

  • Ubiquitination at Lys118
  • Modification sites at PhosphoSitePlus

Other Protein References for PHF6 Gene

No data available for DME Specific Peptides for PHF6 Gene

Domains & Families for PHF6 Gene

Gene Families for PHF6 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for PHF6 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PHF6 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ60207, highly similar to PHD finger protein 6 (B4E0G4_HUMAN)
  • PHD-like zinc finger protein (PHF6_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8IWS0

UniProtKB/Swiss-Prot:

PHF6_HUMAN :
  • The PHD-type zinc finger 1 mediates both nucleolar localization and interaction with UBTF.
Domain:
  • The PHD-type zinc finger 1 mediates both nucleolar localization and interaction with UBTF.
  • The ePHD2 domain folds as an integrated structural module comprizing the C2HC pre-PHD-type 2 zinc finger and the PHD-type 2 zinc finger. It mediates non-specific binding to dsDNA, but doesn't bind histones in contrast to many PHD-type zinc fingers.
genes like me logo Genes that share domains with PHF6: view

Function for PHF6 Gene

Molecular function for PHF6 Gene

UniProtKB/Swiss-Prot Function:
Transcriptional regulator that associates with ribosomal RNA promoters and suppresses ribosomal RNA (rRNA) transcription.

Gene Ontology (GO) - Molecular Function for PHF6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specific IDA 24554700
GO:0003677 DNA binding IEA --
GO:0003723 RNA binding HDA 22658674
GO:0005515 protein binding IPI 22720776
GO:0015631 tubulin binding IPI 22720776
genes like me logo Genes that share ontologies with PHF6: view
genes like me logo Genes that share phenotypes with PHF6: view

Human Phenotype Ontology for PHF6 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PHF6 Gene

MGI Knock Outs for PHF6:
  • Phf6 Phf6<tm1b(EUCOMM)Wtsi>

Animal Model Products

CRISPR Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Transcription Factor Targets and HOMER Transcription for PHF6 Gene

Localization for PHF6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PHF6 Gene

Nucleus. Nucleus, nucleolus. Chromosome, centromere, kinetochore. Note=Nuclear, it particularly localizes to the nucleolus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PHF6 gene
Compartment Confidence
nucleus 5
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
cytosol 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (3)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PHF6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000775 chromosome, centromeric region IEA --
GO:0000776 kinetochore IEA --
GO:0000777 condensed chromosome kinetochore IEA --
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm IDA 22720776
genes like me logo Genes that share ontologies with PHF6: view

Pathways & Interactions for PHF6 Gene

PathCards logo

SuperPathways for PHF6 Gene

genes like me logo Genes that share pathways with PHF6: view

Pathways by source for PHF6 Gene

2 BioSystems pathways for PHF6 Gene

SIGNOR curated interactions for PHF6 Gene

Inactivates:

Gene Ontology (GO) - Biological Process for PHF6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IDA 24554700
GO:0001835 blastocyst hatching IEA --
genes like me logo Genes that share ontologies with PHF6: view

Drugs & Compounds for PHF6 Gene

(1) Drugs for PHF6 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with PHF6: view

Transcripts for PHF6 Gene

mRNA/cDNA for PHF6 Gene

3 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PHF6 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12
SP1: - -
SP2: - -
SP3: -
SP4:
SP5: - -

Relevant External Links for PHF6 Gene

GeneLoc Exon Structure for
PHF6

Expression for PHF6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PHF6 Gene

Protein differential expression in normal tissues from HIPED for PHF6 Gene

This gene is overexpressed in Lung (39.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PHF6 Gene



Protein tissue co-expression partners for PHF6 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PHF6

SOURCE GeneReport for Unigene cluster for PHF6 Gene:

Hs.356501

mRNA Expression by UniProt/SwissProt for PHF6 Gene:

Q8IWS0-PHF6_HUMAN
Tissue specificity: Ubiquitously expressed.

Evidence on tissue expression from TISSUES for PHF6 Gene

  • Nervous system(4.6)
  • Bone marrow(4.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PHF6 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • outer ear
  • skull
Thorax:
  • breast
  • lung
  • rib
  • rib cage
Pelvis:
  • fallopian tube
  • ovary
  • pelvis
  • penis
  • prostate
  • testicle
  • uterus
  • vagina
  • vas deferens
  • vulva
Limb:
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • toe
  • upper limb
General:
  • hair
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with PHF6: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for PHF6 Gene

Orthologs for PHF6 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PHF6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PHF6 31 30
  • 100 (n)
OneToOne
dog
(Canis familiaris)
Mammalia PHF6 31 30
  • 97.63 (n)
OneToOne
cow
(Bos Taurus)
Mammalia PHF6 31 30
  • 95.8 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PHF6 31
  • 95 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PHF6 31
  • 93 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Phf6 17 31 30
  • 92.49 (n)
rat
(Rattus norvegicus)
Mammalia Phf6 30
  • 91.78 (n)
chicken
(Gallus gallus)
Aves PHF6 31 30
  • 84.47 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PHF6 31
  • 87 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia phf6 30
  • 74.75 (n)
Str.15049 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.12568 30
zebrafish
(Danio rerio)
Actinopterygii phf6 31 30
  • 67.32 (n)
OneToOne
wufa22g03 30
Species where no ortholog for PHF6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PHF6 Gene

ENSEMBL:
Gene Tree for PHF6 (if available)
TreeFam:
Gene Tree for PHF6 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PHF6: view image

Paralogs for PHF6 Gene

Paralogs for PHF6 Gene

(1) SIMAP similar genes for PHF6 Gene using alignment to 3 proteins:

  • PHF6_HUMAN
  • B4E0G4_HUMAN
  • Q5JRC6_HUMAN
genes like me logo Genes that share paralogs with PHF6: view

Variants for PHF6 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PHF6 Gene

SNP ID Clinical significance and condition Chr 0X pos Variation AA Info Type
11071 Pathogenic: Borjeson-Forssman-Lehmann syndrome 134,377,997(+) A/G INTRON_VARIANT
11072 Pathogenic: Borjeson-Forssman-Lehmann syndrome 134,377,638(+) G/GA FRAMESHIFT_VARIANT
667852 Likely Benign: not provided 134,413,346(+) T/C INTRON_VARIANT
670935 Benign: not provided 134,377,958(+) G/A INTRON_VARIANT
672755 Benign: not provided 134,413,249(+) A/C INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for PHF6 Gene

Structural Variations from Database of Genomic Variants (DGV) for PHF6 Gene

Variant ID Type Subtype PubMed ID
nsv521188 CNV loss 19592680

Variation tolerance for PHF6 Gene

Residual Variation Intolerance Score: 22% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.28; 6.20% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PHF6 Gene

Human Gene Mutation Database (HGMD)
PHF6
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PHF6

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PHF6 Gene

Disorders for PHF6 Gene

MalaCards: The human disease database

(17) MalaCards diseases for PHF6 Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search PHF6 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PHF6_HUMAN
  • Boerjeson-Forssman-Lehmann syndrome (BFLS) [MIM:301900]: A X-linked recessive disorder characterized by moderate to severe mental retardation, epilepsy, hypogonadism, hypometabolism, obesity with marked gynecomastia, swelling of subcutaneous tissue of the face, narrow palpebral fissure and large but not deformed ears. {ECO:0000269 PubMed:12415272, ECO:0000269 PubMed:23229552, ECO:0000269 PubMed:23906836}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for PHF6

genes like me logo Genes that share disorders with PHF6: view

No data available for Genatlas for PHF6 Gene

Publications for PHF6 Gene

  1. Mutations in PHF6 are associated with Börjeson-Forssman-Lehmann syndrome. (PMID: 12415272) Lower KM … Gécz J (Nature genetics 2002) 2 3 4 23 54
  2. Structural and functional insights into the human Börjeson-Forssman-Lehmann syndrome-associated protein PHF6. (PMID: 24554700) Liu Z … Shi Y (The Journal of biological chemistry 2014) 3 4 54
  3. PHF6 regulates cell cycle progression by suppressing ribosomal RNA synthesis. (PMID: 23229552) Wang J … Chen J (The Journal of biological chemistry 2013) 3 4 54
  4. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4 54
  5. Mutation screening in Borjeson-Forssman-Lehmann syndrome: identification of a novel de novo PHF6 mutation in a female patient. (PMID: 15994862) Crawford J … Gécz J (Journal of medical genetics 2006) 3 23 54

Products for PHF6 Gene

Sources for PHF6 Gene